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Xanthomonas
Infection Transforms the Apoplast into an Accessible and Habitable Niche for Salmonella enterica. Appl Environ Microbiol 2022; 88:e0133022. [PMID: 36314834 PMCID: PMC9680631 DOI: 10.1128/aem.01330-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial spot disease caused by
Xanthomonas
species devastates tomato production worldwide. Salmonellosis outbreaks from consumption of raw produce have been linked to the arrival of
Salmonella enterica
on crop plants in the field via contaminated irrigation water.
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2
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Evaluations of CRC2631 toxicity, tumor colonization, and genetic stability in the TRAMP prostate cancer model. Oncotarget 2020; 11:3943-3958. [PMID: 33216833 PMCID: PMC7646835 DOI: 10.18632/oncotarget.27769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/24/2020] [Indexed: 01/10/2023] Open
Abstract
Conventional cancer chemotherapies are not fully efficacious and do not target tumors, leading to significant treatment-related morbidities. A number of genetically attenuated cancer-targeting bacteria are being developed to safely target tumors in vivo. Here we report the toxicological, tumor-targeting, and efficacy profiles of Salmonella enterica serovar Typhimurium CRC2631 in a syngeneic and autochthonous TRAMP model of aggressive prostate cancer. CRC2631 preferentially colonize primary and metastatic tumors in the TRAMP animals. In addition, longitudinal whole genome sequencing studies of CRC2631 recovered from prostate tumor tissues demonstrate that CRC2631 is genetically stable. Moreover, tumor-targeted CRC2631 generates an anti-tumor immune response. Combination of CRC2631 with checkpoint blockade reduces metastasis burden. Collectively, these findings demonstrate a potential for CRC2631 in cancer immunotherapy strategies.
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3
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Distinct fermentation and antibiotic sensitivity profiles exist in salmonellae of canine and human origin. BMC Microbiol 2018; 18:15. [PMID: 29482521 PMCID: PMC5828451 DOI: 10.1186/s12866-018-1153-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 02/07/2018] [Indexed: 11/10/2022] Open
Abstract
Background Salmonella enterica is a recognised cause of diarrhoea in dogs and humans, yet the potential for transfer of salmonellosis between dogs and their owners is unclear, with reported evidence both for and against Salmonella as a zoonotic pathogen. A collection of 174 S. enterica isolates from clinical infections in humans and dogs were analysed for serotype distribution, carbon source utilisation, chemical and antimicrobial sensitivity profiles. The aim of the study was to understand the degree of conservation in phenotypic characteristics of isolates across host species. Results Serovar distribution across human and canine isolates demonstrated nine serovars common to both host species, 24 serovars present in only the canine collection and 39 solely represented within the human collection. Significant differences in carbon source utilisation profiles and ampicillin, amoxicillin and chloramphenicol sensitivity profiles were detected in isolates of human and canine origin. Differences between the human and canine Salmonella collections were suggestive of evolutionary separation, with canine isolates better able to utilise several simple sugars than their human counterparts. Generally higher minimum inhibitory concentrations of three broad-spectrum antimicrobials, commonly used in veterinary medicine, were also observed in canine S. enterica isolates. Conclusions Differential carbon source utilisation and antimicrobial sensitivity profiles in pathogenic Salmonella isolated from humans and dogs are suggestive of distinct reservoirs of infection for these hosts. Although these findings do not preclude zoonotic or anthroponotic potential in salmonellae, the separation of carbon utilisation and antibiotic profiles with isolate source is indicative that infectious isolates are not part of a common reservoir shared frequently between these host species.
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4
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Medrano-Félix A, Estrada-Acosta M, Peraza-Garay F, Castro-Del Campo N, Martínez-Urtaza J, Chaidez C. Differences in carbon source utilization of Salmonella Oranienburg and Saintpaul isolated from river water. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2017; 27:252-263. [PMID: 28565917 DOI: 10.1080/09603123.2017.1332349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 05/15/2017] [Indexed: 06/07/2023]
Abstract
Long-term exposure to river water by non-indigenous micro-organisms such as Salmonella may affect metabolic adaptation to carbon sources. This study was conducted to determine differences in carbon source utilization of Salmonella Oranienburg and Salmonella Saintpaul (isolated from tropical river water) as well as the control strain Salmonella Typhimurium exposed to laboratory, river water, and host cells (Hep-2 cell line) growth conditions. Results showed that Salmonella Oranienburg and Salmonella Saintpaul showed better ability for carbon source utilization under the three growth conditions evaluated; however, S. Oranienburg showed the fastest and highest utilization on different carbon sources, including D-Glucosaminic acid, N-acetyl-D-Glucosamine, Glucose-1-phosphate, and D-Galactonic acid, while Salmonella Saintpaul and S. Typhimurium showed a limited utilization of carbon sources. In conclusion, this study suggests that environmental Salmonella strains show better survival and preconditioning abilities to external environments than the control strain based on their plasticity on diverse carbon sources use.
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Affiliation(s)
- Andrés Medrano-Félix
- a CONACYT-Centro de Investigación en Alimentación y Desarrollo A.C. , Coordinación Regional Culiacán, Laboratorio Nacional para la Investigación en Inocuidad Alimentaria. Culiacán , Sinaloa , México
| | | | - Felipe Peraza-Garay
- c Centro de Investigación y Docencia en Ciencias de la Salud , Universidad Autónoma de Sinaloa , Sinaloa , México
| | - Nohelia Castro-Del Campo
- d Centro de Investigación en Alimentación y Desarrollo A.C. , Coordinación Regional Culiacán Laboratorio Nacional para la Investigación en Inocuidad Alimentaria. Culiacán , Sinaloa , México
| | | | - Cristóbal Chaidez
- d Centro de Investigación en Alimentación y Desarrollo A.C. , Coordinación Regional Culiacán Laboratorio Nacional para la Investigación en Inocuidad Alimentaria. Culiacán , Sinaloa , México
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5
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Greetham D, Lappin DF, Rajendran R, O'Donnell L, Sherry L, Ramage G, Nile C. The application of phenotypic microarray analysis to anti-fungal drug development. J Microbiol Methods 2017; 134:35-37. [PMID: 28082175 DOI: 10.1016/j.mimet.2017.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/06/2017] [Accepted: 01/06/2017] [Indexed: 10/20/2022]
Abstract
Candida albicans metabolic activity in the presence and absence of acetylcholine was measured using phenotypic microarray analysis. Acetylcholine inhibited C. albicans biofilm formation by slowing metabolism independent of biofilm forming capabilities. Phenotypic microarray analysis can therefore be used for screening compound libraries for novel anti-fungal drugs and measuring antifungal resistance.
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Affiliation(s)
- Darren Greetham
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - David F Lappin
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
| | - Ranjith Rajendran
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
| | - Lindsay O'Donnell
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
| | - Leighann Sherry
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
| | - Gordon Ramage
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
| | - Christopher Nile
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK.
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6
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Feasey NA, Hadfield J, Keddy KH, Dallman TJ, Jacobs J, Deng X, Wigley P, Barquist L, Langridge GC, Feltwell T, Harris SR, Mather AE, Fookes M, Aslett M, Msefula C, Kariuki S, Maclennan CA, Onsare RS, Weill FX, Le Hello S, Smith AM, McClelland M, Desai P, Parry CM, Cheesbrough J, French N, Campos J, Chabalgoity JA, Betancor L, Hopkins KL, Nair S, Humphrey TJ, Lunguya O, Cogan TA, Tapia MD, Sow SO, Tennant SM, Bornstein K, Levine MM, Lacharme-Lora L, Everett DB, Kingsley RA, Parkhill J, Heyderman RS, Dougan G, Gordon MA, Thomson NR. Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings. Nat Genet 2016; 48:1211-1217. [PMID: 27548315 PMCID: PMC5047355 DOI: 10.1038/ng.3644] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 07/15/2016] [Indexed: 11/15/2022]
Abstract
An epidemiological paradox surrounds Salmonella enterica serovar Enteritidis. In high-income settings, it has been responsible for an epidemic of poultry-associated, self-limiting enterocolitis, whereas in sub-Saharan Africa it is a major cause of invasive nontyphoidal Salmonella disease, associated with high case fatality. By whole-genome sequence analysis of 675 isolates of S. Enteritidis from 45 countries, we show the existence of a global epidemic clade and two new clades of S. Enteritidis that are geographically restricted to distinct regions of Africa. The African isolates display genomic degradation, a novel prophage repertoire, and an expanded multidrug resistance plasmid. S. Enteritidis is a further example of a Salmonella serotype that displays niche plasticity, with distinct clades that enable it to become a prominent cause of gastroenteritis in association with the industrial production of eggs and of multidrug-resistant, bloodstream-invasive infection in Africa.
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Affiliation(s)
- Nicholas A Feasey
- Liverpool School of Tropical Medicine, Liverpool, UK
- Wellcome Trust Sanger Institute, Cambridge, UK
- Malawi Liverpool Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | | | - Karen H Keddy
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Timothy J Dallman
- Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, UK
| | - Jan Jacobs
- Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology and Immunology, University of Leuven, Belgium
| | - Xiangyu Deng
- Center for Food Safety, Department of Food Science and Technology, University of Georgia
- Centers for Disease Control and Prevention, Atlanta, USA
| | - Paul Wigley
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Lars Barquist
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | | | | | | | | | | | | | - Chisomo Msefula
- Malawi Liverpool Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- University of Malawi, The College of Medicine, Blantyre, Malawi
| | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Calman A Maclennan
- Wellcome Trust Sanger Institute, Cambridge, UK
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Robert S Onsare
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | | | | | - Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA, USA
| | - Prerak Desai
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA, USA
| | - Christopher M Parry
- Liverpool School of Tropical Medicine, Liverpool, UK
- London School of Hygiene & Tropical Medicine, London, UK
| | - John Cheesbrough
- Department of Epidemiology and Population Health, University of Liverpool, Liverpool, UK
| | - Neil French
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Josefina Campos
- Enteropathogen Division, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) Carlos G. Malbran Institute, Buenos Aires, Argentina
| | - Jose A Chabalgoity
- Instituto de Higiene, Facultad de Medicina, Universidad de la Republica, Uruguay
| | - Laura Betancor
- Instituto de Higiene, Facultad de Medicina, Universidad de la Republica, Uruguay
| | - Katie L Hopkins
- Antimicrobial Resistance and Healthcare-Associated Infections Reference Unit, Public Health England, Colindale, UK
| | - Satheesh Nair
- Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, UK
| | | | - Octavie Lunguya
- National Institute of Biomedical Research, Kinshasa, the Democratic Republic of the Congo
- University Hospital of Kinshasa, Kinshasa, the Democratic Republic of the Congo
| | - Tristan A Cogan
- School of Veterinary Sciences, University of Bristol, Bristol, UK
| | - Milagritos D Tapia
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Samba O Sow
- Centre pour le Développement des Vaccins, Bamako, Mali
| | - Sharon M Tennant
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Kristin Bornstein
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Myron M Levine
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Lizeth Lacharme-Lora
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Dean B Everett
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Robert A Kingsley
- Wellcome Trust Sanger Institute, Cambridge, UK
- Institute of Food Research, Colney, Norwich, UK
| | | | - Robert S Heyderman
- Malawi Liverpool Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Division of Infection and Immunity, University College London, London, UK
| | | | - Melita A Gordon
- Malawi Liverpool Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Nicholas R Thomson
- Wellcome Trust Sanger Institute, Cambridge, UK
- London School of Hygiene & Tropical Medicine, London, UK
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7
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Bloodworth RAM, Zlitni S, Brown ED, Cardona ST. An electron transfer flavoprotein is essential for viability and its depletion causes a rod-to-sphere change in Burkholderia cenocepacia. MICROBIOLOGY-SGM 2015; 161:1909-1920. [PMID: 26253539 DOI: 10.1099/mic.0.000156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Essential gene studies often reveal novel essential functions for genes with dispensable homologues in other species. This is the case with the widespread family of electron transfer flavoproteins (ETFs), which are required for the metabolism of specific substrates or for symbiotic nitrogen fixation in some bacteria. Despite these non-essential functions high-throughput screens have identified ETFs as putatively essential in several species. In this study, we constructed a conditional expression mutant of one of the ETFs in Burkholderia cenocepacia, and demonstrated that its expression is essential for growth on both complex media and a variety of single-carbon sources. We further demonstrated that the two subunits EtfA and EtfB interact with each other, and that cells depleted of ETF are non-viable and lack redox potential. These cells also transition from the short rods characteristic of Burkholderia cenocepacia to small spheres independently of MreB. The putative membrane partner ETF dehydrogenase also induced the same rod-to-sphere change. We propose that the ETF of Burkholderia cenocepacia is a novel antibacterial target.
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Affiliation(s)
| | - Soumaya Zlitni
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Eric D Brown
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Silvia T Cardona
- Department of Microbiology, University of Manitoba, Winnipeg, Canada.,Department of Medical Microbiology & Infectious Disease, University of Manitoba, Winnipeg, Canada
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8
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Bourne CR, Wakeham N, Bunce RA, Berlin KD, Barrow WW. Classifying compound mechanism of action for linking whole cell phenotypes to molecular targets. J Mol Recognit 2012; 25:216-23. [PMID: 22434711 PMCID: PMC3703735 DOI: 10.1002/jmr.2174] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Drug development programs have proven successful when performed at a whole cell level, thus incorporating solubility and permeability into the primary screen. However, linking those results to the target within the cell has been a major setback. The Phenotype Microarray system, marketed and sold by Biolog, seeks to address this need by assessing the phenotype in combination with a variety of chemicals with known mechanism of action (MOA). We have evaluated this system for usefulness in deducing the MOA for three test compounds. To achieve this, we constructed a database with 21 known antimicrobials, which served as a comparison for grouping our unknown MOA compounds. Pearson correlation and Ward linkage calculations were used to generate a dendrogram that produced clustering largely by known MOA, although there were exceptions. Of the three unknown compounds, one was definitively placed as an antifolate. The second and third compounds' MOA were not clearly identified, likely because the unique MOA was not represented within the database. The availability of the database generated in this report for Staphylococcus aureus ATCC 29213 will increase the accessibility of this technique to other investigators. From our analysis, the Phenotype Microarray system can group compounds with clear MOA, but the distinction of unique or broadly acting MOA at this time is less clear.
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Affiliation(s)
- Christina R. Bourne
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater OK 74078
| | - Nancy Wakeham
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater OK 74078
| | - Richard A. Bunce
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences 1, Stillwater OK 74078
| | - K. Darrell Berlin
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences 1, Stillwater OK 74078
| | - William W. Barrow
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater OK 74078
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9
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Eisenstark A. Genetic diversity among offspring from archived Salmonella enterica ssp. enterica serovar typhimurium (Demerec Collection): in search of survival strategies. Annu Rev Microbiol 2010; 64:277-92. [PMID: 20825350 DOI: 10.1146/annurev.micro.091208.073614] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Extensive phenotypic and genomic diversity was detected among offspring of Salmonella enterica ssp. enterica serovar Typhimurium LT2 (nonmutator) and LT7 (mutator, mutL) strains after decades of storage in sealed nutrient agar stabs. In addition to numerous losses in carbon and nitrogen metabolism, the acquired new metabolites indicated that alternate pathways were established. Particularly striking was the array of phage types when this phenotype was expected to be a stable feature. Evidence is presented regarding the role of mutator gene mutL(-) in the establishment of diversity as well as the ability of cells to return to mutL(+) genetic stabilization. Mutations included deletions, duplications, frameshifts, inversions and transpositions. In competition tests, survivors were more fit than were wild type. Because survival strategies continue to intrigue microbiologists, observations are compared with those of others who have addressed related questions. A brief genealogy of the archived strains is also recorded.
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Affiliation(s)
- Abraham Eisenstark
- Cancer Research Center and Division of Biological Sciences, University of Missouri, Columbia, Missouri 65201, USA.
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10
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Metabolic capacity of Sinorhizobium (Ensifer) meliloti strains as determined by phenotype MicroArray analysis. Appl Environ Microbiol 2009; 75:5396-404. [PMID: 19561177 DOI: 10.1128/aem.00196-09] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sinorhizobium meliloti is a soil bacterium that fixes atmospheric nitrogen in plant roots. The high genetic diversity of its natural populations has been the subject of extensive analysis. Recent genomic studies of several isolates revealed a high content of variable genes, suggesting a correspondingly large phenotypic differentiation among strains of S. meliloti. Here, using the Phenotype MicroArray (PM) system, hundreds of different growth conditions were tested in order to compare the metabolic capabilities of the laboratory reference strain Rm1021 with those of four natural S. meliloti isolates previously analyzed by comparative genomic hybridization (CGH). The results of PM analysis showed that most phenotypic differences involved carbon source utilization and tolerance to osmolytes and pH, while fewer differences were scored for nitrogen, phosphorus, and sulfur source utilization. Only the variability of the tested strain in tolerance to sodium nitrite and ammonium sulfate of pH 8 was hypothesized to be associated with the genetic polymorphisms detected by CGH analysis. Colony and cell morphologies and the ability to nodulate Medicago truncatula plants were also compared, revealing further phenotypic diversity. Overall, our results suggest that the study of functional (phenotypic) variability of S. meliloti populations is an important and complementary step in the investigation of genetic polymorphism of rhizobia and may help to elucidate rhizobial evolutionary dynamics, including adaptation to diverse environments.
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11
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Bochner BR. Global phenotypic characterization of bacteria. FEMS Microbiol Rev 2009; 33:191-205. [PMID: 19054113 PMCID: PMC2704929 DOI: 10.1111/j.1574-6976.2008.00149.x] [Citation(s) in RCA: 293] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 10/06/2008] [Accepted: 10/24/2008] [Indexed: 11/30/2022] Open
Abstract
The measure of the quality of a systems biology model is how well it can reproduce and predict the behaviors of a biological system such as a microbial cell. In recent years, these models have been built up in layers, and each layer has been growing in sophistication and accuracy in parallel with a global data set to challenge and validate the models in predicting the content or activities of genes (genomics), proteins (proteomics), metabolites (metabolomics), and ultimately cell phenotypes (phenomics). This review focuses on the latter, the phenotypes of microbial cells. The development of Phenotype MicroArrays, which attempt to give a global view of cellular phenotypes, is described. In addition to their use in fleshing out and validating systems biology models, there are many other uses of this global phenotyping technology in basic and applied microbiology research, which are also described.
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12
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Eisenstark A, Kazmierczak RA, Dino A, Khreis R, Newman D, Schatten H. Development of Salmonella strains as cancer therapy agents and testing in tumor cell lines. Methods Mol Biol 2007; 394:323-354. [PMID: 18363243 DOI: 10.1007/978-1-59745-512-1_16] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Despite significant progress in the development of new drugs and radiation, deaths due to cancer remain high. Many novel therapies are in clinical trials and offer better solutions, but more innovative approaches are needed to eradicate the various subpopulations that exist in solid tumors. Since 1997, the use of bacteria for cancer therapy has gained increased attention. Salmonella Typhimurium strains have been shown to have a remarkably high affinity for tumor cells. The use of bacterial strains to target tumors is a relatively new research method that has not yet reached the point of clinical success. The first step in assessing the effectiveness of bacterial tumor therapy will require strain development and preclinical comparisons of candidate strains, which is the focus of this chapter. Several investigators have developed strains of Salmonella with reduced toxicity and capacity to deliver anti-tumor agents. Although methods for obtaining safe therapeutic strains have been relatively successful, there is still need for further genetic engineering before successful clinical use in human patients. As described by Forbes et al. in 2003, the main stumbling block is that, while bacteria preferentially embed within tumor cells, they fail to spread within the tumor and finish the eradication process. Further engineering might focus on creating Salmonella that remove motility limitations, including increased affinity toward tumor-generated chemotactic attractants and induction of matrix-degrading enzymes.
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Affiliation(s)
- Abraham Eisenstark
- Cancer Research Center and Division of Biological Sciences, University of Missouri, Columbia, USA
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13
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Abstract
The traditional view of the stationary phase of the bacterial life cycle, obtained using standard laboratory culture practices, although useful, might not always provide us with the complete picture. Here, the traditional three phases of the bacterial life cycle are expanded to include two additional phases: death phase and long-term stationary phase. In many natural environments, bacteria probably exist in conditions more akin to those of long-term stationary-phase cultures, in which the expression of a wide variety of stress-response genes and alternative metabolic pathways is essential for survival. Furthermore, stressful environments can result in selection for mutants that express the growth advantage in stationary phase (GASP) phenotype.
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Affiliation(s)
- Steven E Finkel
- Molecular and Computational Biology Programme, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-2910, USA.
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14
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Nishino K, Honda T, Yamaguchi A. Genome-wide analyses of Escherichia coli gene expression responsive to the BaeSR two-component regulatory system. J Bacteriol 2005; 187:1763-72. [PMID: 15716448 PMCID: PMC1063996 DOI: 10.1128/jb.187.5.1763-1772.2005] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The BaeSR two-component regulatory system controls expression of exporter genes conferring drug resistance in Escherichia coli (S. Nagakubo, K. Nishino, T. Hirata, and A. Yamaguchi, J. Bacteriol. 184:4161-4167, 2002; N. Baranova and H. Nikaido, J. Bacteriol. 184:4168-4176, 2002). To understand the whole picture of BaeSR regulation, a DNA microarray analysis of the effect of BaeR overproduction was performed. BaeR overproduction activated 59 genes related to two-component signal transduction, chemotactic responses, flagellar biosynthesis, maltose transport, and multidrug transport, and BaeR overproduction also repressed the expression of the ibpA and ibpB genes. All of the changes in the expression levels were also observed by quantitative real-time reverse transcription-PCR analysis. The expression levels of 15 of the 59 BaeR-activated genes were decreased by deletion of baeSR. Of 11 genes induced by indole (a putative inducer of the BaeSR system), 10 required the BaeSR system for induction. Combination of the expression data sets revealed a BaeR-binding site sequence motif, 5'-TTTTTCTCCATDATTGGC-3' (where D is G, A, or T). Several genes up-regulated by BaeR overproduction, including genes for maltose transport, chemotactic responses, and flagellar biosynthesis, required an intact PhoBR or CreBC two-component regulatory system for up-regulation. These data indicate that there is cross-regulation among the BaeSR, PhoBR, and CreBC two-component regulatory systems. Such a global analysis should reveal the regulatory network of the BaeSR system.
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Affiliation(s)
- Kunihiko Nishino
- Department of Cell Membrane Biology, Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
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15
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Rabsch W, Helm RA, Eisenstark A. Diversity of phage types among archived cultures of the Demerec collection of Salmonella enterica serovar Typhimurium strains. Appl Environ Microbiol 2004; 70:664-9. [PMID: 14766539 PMCID: PMC348941 DOI: 10.1128/aem.70.2.664-669.2004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The existence of several thousand Salmonella enterica serovar Typhimurium LT2 and LT7 cultures originally collected by M. Demerec and sealed in agar stab vials for 33 to 46 years is a resource for evolutionary and mutational studies. Cultures from 74 of these vials, descendants of cells sealed and stored in nutrient agar stabs several decades ago, were phage typed by the Callow and Felix, Lilleengen, and Anderson systems. Among 53 LT2 archived strains, 16 had the same phage type as the nonarchival sequenced LT2 strain. The other 37 archived cultures differed in phage typing pattern from the sequenced strain. These 37 strains were divided into 10 different phage types. Among the 19 LT7 strains, only one was similar to the parent by phage typing, while 18 were different. These 18 strains fell into eight different phage types. The typing systems were developed to track epidemics from source to consumer, as well as geographic spread. The value of phage typing is dependent upon the stability of the phage type of any given strain throughout the course of the investigation. Thus, the variation over time observed in these archived cultures is particularly surprising. Possible mechanisms for such striking diversity may include loss of prophages, prophage mosaics as a result of recombination events, changes in phage receptor sites on the bacterial cell surface, or mutations in restriction-modification systems.
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Affiliation(s)
- Wolfgang Rabsch
- National Reference Centre for Salmonella and Other Enterics, Robert Koch Institute, Wernigerode Branch, D-38855 Wernigerode, Germany
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Porwollik S, Wong RMY, Helm RA, Edwards KK, Calcutt M, Eisenstark A, McClelland M. DNA amplification and rearrangements in archival Salmonella enterica serovar Typhimurium LT2 cultures. J Bacteriol 2004; 186:1678-82. [PMID: 14996798 PMCID: PMC355959 DOI: 10.1128/jb.186.6.1678-1682.2004] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Variations in genome size and gene order were observed in archival Salmonella enterica serovar Typhimurium cultures stored for over 40 years. In one strain, microarray analysis revealed a large, stable amplification. PCR analysis of the same strain revealed a genomic duplication that underwent a translocation. Other strains had smaller duplications and deletions. These results demonstrate that storage in stabs over time at room temperature not only allows for further bacterial growth but also may produce an environment that selects for a variety of mutations, including genomic rearrangements.
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Zhou L, Lei XH, Bochner BR, Wanner BL. Phenotype microarray analysis of Escherichia coli K-12 mutants with deletions of all two-component systems. J Bacteriol 2003; 185:4956-72. [PMID: 12897016 PMCID: PMC166450 DOI: 10.1128/jb.185.16.4956-4972.2003] [Citation(s) in RCA: 235] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two-component systems are the most common mechanism of transmembrane signal transduction in bacteria. A typical system consists of a histidine kinase and a partner response regulator. The histidine kinase senses an environmental signal, which it transmits to its partner response regulator via a series of autophosphorylation, phosphotransfer, and dephosphorylation reactions. Much work has been done on particular systems, including several systems with regulatory roles in cellular physiology, communication, development, and, in the case of bacterial pathogens, the expression of genes important for virulence. We used two methods to investigate two-component regulatory systems in Escherichia coli K-12. First, we systematically constructed mutants with deletions of all two-component systems by using a now-standard technique of gene disruption (K. A. Datsenko and B. L. Wanner, Proc. Natl. Acad. Sci. USA 97:6640-6645, 2000). We then analyzed these deletion mutants with a new technology called Phenotype MicroArrays, which permits assays of nearly 2,000 growth phenotypes simultaneously. In this study we tested 100 mutants, including mutants with individual deletions of all two-component systems and several related genes, including creBC-regulated genes (cbrA and cbrBC), phoBR-regulated genes (phoA, phoH, phnCDEFGHIJKLMNOP, psiE, and ugpBAECQ), csgD, luxS, and rpoS. The results of this battery of nearly 200,000 tests provided a wealth of new information concerning many of these systems. Of 37 different two-component mutants, 22 showed altered phenotypes. Many phenotypes were expected, and several new phenotypes were also revealed. The results are discussed in terms of the biological roles and other information concerning these systems, including DNA microarray data for a large number of the same mutants. Other mutational effects are also discussed.
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Affiliation(s)
- Lu Zhou
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
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